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Chen H, Wang Y, Wang W, Cao T, Zhang L, Wang Z, Chi X, Shi T, Wang H, He X, Liang M, Yang M, Jiang W, Lv D, Yu J, Zhu G, Xie Y, Gao B, Wang X, Liu X, Li Y, Ouyang L, Zhang J, Liu H, Li Z, Tong Y, Xia X, Tan GY, Zhang L. High-yield porphyrin production through metabolic engineering and biocatalysis. Nat Biotechnol 2024:10.1038/s41587-024-02267-3. [PMID: 38839873 DOI: 10.1038/s41587-024-02267-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024]
Abstract
Porphyrins and their derivatives find extensive applications in medicine, food, energy and materials. In this study, we produced porphyrin compounds by combining Rhodobacter sphaeroides as an efficient cell factory with enzymatic catalysis. Genome-wide CRISPRi-based screening in R. sphaeroides identifies hemN as a target for improved coproporphyrin III (CPIII) production, and exploiting phosphorylation of PrrA further improves the production of bioactive CPIII to 16.5 g L-1 by fed-batch fermentation. Subsequent screening and engineering high-activity metal chelatases and coproheme decarboxylase results in the synthesis of various metalloporphyrins, including heme and the anti-tumor agent zincphyrin. After pilot-scale fermentation (200 L) and setting up the purification process for CPIII (purity >95%), we scaled up the production of heme and zincphyrin through enzymatic catalysis in a 5-L bioreactor, with CPIII achieving respective enzyme conversion rates of 63% and 98% and yielding 10.8 g L-1 and 21.3 g L-1, respectively. Our strategy offers a solution for high-yield bioproduction of heme and other valuable porphyrins with substantial industrial and medical applications.
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Affiliation(s)
- Haihong Chen
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yaohong Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ting Cao
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xuran Chi
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Tong Shi
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Huangwei Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xinwei He
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mindong Liang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Mengxue Yang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Wenyi Jiang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Dongyuan Lv
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jiaming Yu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Yongtao Xie
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Youyuan Li
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Limin Ouyang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Huimin Liu
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yaojun Tong
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuekui Xia
- Key Biosensor Laboratory of Shandong Province, Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China.
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering and School of Biotechnology, East China University of Science and Technology, Shanghai, China.
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Chadha R, Guerrero JA, Wei L, Sanchez LM. Seeing is Believing: Developing Multimodal Metabolic Insights at the Molecular Level. ACS CENTRAL SCIENCE 2024; 10:758-774. [PMID: 38680555 PMCID: PMC11046475 DOI: 10.1021/acscentsci.3c01438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 05/01/2024]
Abstract
This outlook explores how two different molecular imaging approaches might be combined to gain insight into dynamic, subcellular metabolic processes. Specifically, we discuss how matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and stimulated Raman scattering (SRS) microscopy, which have significantly pushed the boundaries of imaging metabolic and metabolomic analyses in their own right, could be combined to create comprehensive molecular images. We first briefly summarize the recent advances for each technique. We then explore how one might overcome the inherent limitations of each individual method, by envisioning orthogonal and interchangeable workflows. Additionally, we delve into the potential benefits of adopting a complementary approach that combines both MSI and SRS spectro-microscopy for informing on specific chemical structures through functional-group-specific targets. Ultimately, by integrating the strengths of both imaging modalities, researchers can achieve a more comprehensive understanding of biological and chemical systems, enabling precise metabolic investigations. This synergistic approach holds substantial promise to expand our toolkit for studying metabolites in complex environments.
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Affiliation(s)
- Rahuljeet
S Chadha
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125 United States
| | - Jason A. Guerrero
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa
Cruz, California 95064 United States
| | - Lu Wei
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125 United States
| | - Laura M. Sanchez
- Department
of Chemistry and Biochemistry, University
of California, Santa Cruz, Santa
Cruz, California 95064 United States
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3
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Ye R, Biango-Daniels M, Steenwyk JL, Rokas A, Louw NL, Nardella R, Wolfe BE. Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet Biol 2024; 171:103862. [PMID: 38218228 DOI: 10.1016/j.fgb.2023.103862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/06/2023] [Accepted: 12/23/2023] [Indexed: 01/15/2024]
Abstract
Although Penicillium molds can have significant impacts on agricultural, industrial, and biomedical systems, the ecological roles of Penicillium species in many microbiomes are not well characterized. Here we utilized a collection of 35 Penicillium strains isolated from cheese rinds to broadly investigate the genomic potential for secondary metabolism in cheese-associated Penicillium species, the impact of Penicillium on bacterial community assembly, and mechanisms of Penicillium-bacteria interactions. Using antiSMASH, we identified 1558 biosynthetic gene clusters, 406 of which were mapped to known pathways, including several mycotoxins and antimicrobial compounds. By measuring bacterial abundance and fungal mRNA expression when culturing representative Penicillium strains with a cheese rind bacterial community, we observed divergent impacts of different Penicillium strains, from strong inhibitors of bacterial growth to those with no impact on bacterial growth or community composition. Through differential mRNA expression analyses, Penicillium strains demonstrated limited differential gene expression in response to the bacterial community. We identified a few shared responses between the eight tested Penicillium strains, primarily upregulation of nutrient metabolic pathways, but we did not identify a conserved fungal response to growth in a multispecies community. These results in tandem suggest high variation among cheese-associated Penicillium species in their ability to shape bacterial community development and highlight important ecological diversity within this iconic genus.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Jacob L Steenwyk
- Department of Molecular and Cellular Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Nicolas L Louw
- Department of Biology, Tufts University, Medford, MA, USA
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4
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Rodríguez J, Vázquez L, Flórez AB, Mayo B. Epicoccum sp. as the causative agent of a reddish-brown spot defect on the surface of a hard cheese made of raw ewe milk. Int J Food Microbiol 2023; 406:110401. [PMID: 37722266 DOI: 10.1016/j.ijfoodmicro.2023.110401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/29/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Colour defects can affect the appearance of cheese, its flavour, the safety of its consumption, and the price it can demand. This work reports the identification of five fungal isolates from a dairy plant where the surface of most cheeses was affected by patent, reddish-to-brown stains. One of these isolates was obtained from cheese, two from brine, and two from a bulk tank containing ewe milk. Molecular identification by partial amplification, sequencing, and database comparison of the concatenated sequence of the genes coding for the largest subunit of RNA polymerase II (RPB2), β-tubulin (β-TUB), and the large subunit of the rRNA molecule (LSU), plus the internal transcribed sequence (ITS) regions, assigned the isolates to Epicoccum layuense, Epicoccum italicum, and Epicoccum mezzettii. Features of the growth of these different species on different agar-based media, and of the morphology of their conidia following sporulation, are also reported. The strain isolated from cheese, E. layuense IPLA 35011, was able to recreate the reddish-brown stains on slices of Gouda-like cheese, which linked the fungus with the colour defect. In addition, two other strains, E. italicum IPLA 35013 from brine and E. italicum IPLA 35014 from milk, also produced stains on cheese slices. Epicoccum species are widely recognized as plant pathogens but have seldom been reported in the dairy setting, and never as human or animal pathogens.
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Affiliation(s)
- Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain.
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5
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McAtamney A, Heaney C, Lizama-Chamu I, Sanchez LM. Reducing Mass Confusion over the Microbiome. Anal Chem 2023; 95:16775-16785. [PMID: 37934885 PMCID: PMC10841885 DOI: 10.1021/acs.analchem.3c02408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
As genetic tools continue to emerge and mature, more information is revealed about the identity and diversity of microbial community members. Genetic tools can also be used to make predictions about the chemistry that bacteria and fungi produce to function and communicate with one another and the host. Ongoing efforts to identify these products and link genetic information to microbiome chemistry rely on analytical tools. This tutorial highlights recent advancements in microbiome studies driven by techniques in mass spectrometry.
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Affiliation(s)
- Allyson McAtamney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Casey Heaney
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Itzel Lizama-Chamu
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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6
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Ye R, Tomo C, Chan N, Wolfe BE. Penicillium molds impact the transcriptome and evolution of the cheese bacterium Staphylococcus equorum. mSphere 2023; 8:e0004723. [PMID: 37219436 PMCID: PMC10449494 DOI: 10.1128/msphere.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023] Open
Abstract
The observation that Penicillium molds can inhibit the growth of Staphylococcus was a catalyst for the antibiotic revolution. Considerable attention has been paid to purified Penicillium metabolites that inhibit bacteria, but little is known about how Penicillium species impact the ecology and evolution of bacteria in multispecies microbial communities. Here, we investigated how four different species of Penicillium can impact global transcription and evolution of a widespread Staphylococcus species (S. equorum) using the cheese rind model microbiome. Through RNA sequencing, we identified a core transcriptional response of S. equorum against all five tested Penicillium strains, including upregulation of thiamine biosynthesis, fatty acid degradation, and amino acid metabolism as well as downregulation of genes involved in the transport of siderophores. In a 12-week evolution experiment where we co-cultured S. equorum with the same Penicillium strains, we observed surprisingly few non-synonymous mutations across S. equorum populations evolved with the Penicillium species. A mutation in a putative DHH family phosphoesterase gene only occurred in populations evolved without Penicillium and decreased the fitness of S. equorum when co-cultured with an antagonistic Penicillium strain. Our results highlight the potential for conserved mechanisms of Staphylococcus-Penicillium interactions and demonstrate how fungal biotic environments may constrain the evolution of bacterial species.IMPORTANCEFungi and bacteria are commonly found co-occurring both in natural and synthetic microbiomes, but our understanding of fungal-bacterial interactions is limited to a handful of species. Conserved mechanisms of interactions and evolutionary consequences of fungal-bacterial interactions are largely unknown. Our RNA sequencing and experimental evolution data with Penicillium species and the bacterium S. equorum demonstrate that divergent fungal species can elicit conserved transcriptional and genomic responses in co-occurring bacteria. Penicillium molds are integral to the discovery of novel antibiotics and production of certain foods. By understanding how Penicillium species affect bacteria, our work can further efforts to design and manage Penicillium-dominated microbial communities in industry and food production.
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Affiliation(s)
- Ruby Ye
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Christopher Tomo
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Neal Chan
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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7
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Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. Analyst 2023; 148:3002-3018. [PMID: 37259951 PMCID: PMC10330857 DOI: 10.1039/d3an00408b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.
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Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612, USA
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Celine A Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, USA
- Tufts University Sensory and Science Center, Medford, Massachusetts, 02155, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093, USA
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
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8
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Rodríguez J, Lobato C, Vázquez L, Mayo B, Flórez AB. Prodigiosin-Producing Serratia marcescens as the Causal Agent of a Red Colour Defect in a Blue Cheese. Foods 2023; 12:2388. [PMID: 37372599 DOI: 10.3390/foods12122388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Technological defects in the organoleptic characteristics of cheese (odour, colour, texture, and flavour) reduce quality and consumer acceptance. A red colour defect in Cabrales cheese (a traditional, blue-veined, Spanish cheese made from raw milk) occurs infrequently but can have a notable economic impact on family-owned, artisanal cheesemaking businesses. This work reports the culture-based determination of Serratia marcescens as the microbe involved in the appearance of red spots on the surface and nearby inner areas of such cheese. Sequencing and analysis of the genome of one S. marcescens isolate, RO1, revealed a cluster of 16 genes involved in the production of prodigiosin, a tripyrrole red pigment. HPLC analysis confirmed the presence of prodigiosin in methanol extracts of S. marcescens RO1 cultures. The same was also observed in extracts from red areas of affected cheeses. The strain showed low survival rates under acidic conditions but was not affected by concentrations of up to 5% NaCl (the usual value for blue cheese). The optimal conditions for prodigiosin production by S. marscescens RO1 on agar plates were 32 °C and aerobic conditions. Prodigiosin has been reported to possess antimicrobial activity, which agrees with the here-observed inhibitory effect of RO1 supernatants on different bacteria, the inhibition of Enterobacteriaceae, and the delayed development of Penicillium roqueforti during cheesemaking. The association between S. marcescens and the red colour defect was strengthened by recreating the fault in experimental cheeses inoculated with RO1. The data gathered in this study point towards the starting milk as the origin of this bacterium in cheese. These findings should help in the development of strategies that minimize the incidence of pigmenting S. marcescens in milk, the red defect the bacterium causes in cheese, and its associated economic losses.
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Affiliation(s)
- Javier Rodríguez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Cristina Lobato
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
| | - Lucía Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
| | - Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011 Oviedo, Spain
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9
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Tannous J, Cosetta CM, Drott MT, Rush TA, Abraham PE, Giannone RJ, Keller NP, Wolfe BE. LaeA-Regulated Fungal Traits Mediate Bacterial Community Assembly. mBio 2023:e0076923. [PMID: 37162223 DOI: 10.1128/mbio.00769-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Potent antimicrobial metabolites are produced by filamentous fungi in pure culture, but their ecological functions in nature are often unknown. Using an antibacterial Penicillium isolate and a cheese rind microbial community, we demonstrate that a fungal specialized metabolite can regulate the diversity of bacterial communities. Inactivation of the global regulator, LaeA, resulted in the loss of antibacterial activity in the Penicillium isolate. Cheese rind bacterial communities assembled with the laeA deletion strain had significantly higher bacterial abundances than the wild-type strain. RNA-sequencing and metabolite profiling demonstrated a striking reduction in the expression and production of the natural product pseurotin in the laeA deletion strain. Inactivation of a core gene in the pseurotin biosynthetic cluster restored bacterial community composition, confirming the role of pseurotins in mediating bacterial community assembly. Our discovery demonstrates how global regulators of fungal transcription can control the assembly of bacterial communities and highlights an ecological role for a widespread class of fungal specialized metabolites. IMPORTANCE Cheese rinds are economically important microbial communities where fungi can impact food quality and aesthetics. The specific mechanisms by which fungi can regulate bacterial community assembly in cheeses, other fermented foods, and microbiomes in general are largely unknown. Our study highlights how specialized metabolites secreted by a Penicillium species can mediate cheese rind development via differential inhibition of bacterial community members. Because LaeA regulates specialized metabolites and other ecologically relevant traits in a wide range of filamentous fungi, this global regulator may have similar impacts in other fungus-dominated microbiomes.
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Affiliation(s)
- Joanna Tannous
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Casey M Cosetta
- Department of Biology, Tufts University, Medford, Massachusetts, USA
| | - Milton T Drott
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- USDA-ARS Cereal Disease Laboratory, St. Paul, Minnesota, USA
| | - Tomás A Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, USA
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10
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Cui F, Fan R, Wang D, Li J, Li T. Research progress on iron uptake pathways and mechanisms of foodborne microorganisms and their application in the food sector. Crit Rev Food Sci Nutr 2023:1-19. [PMID: 37099732 DOI: 10.1080/10408398.2023.2204491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Iron is one of the essential nutrients for almost all microorganisms. Under iron-limited conditions, bacteria can secrete siderophores to the outside world to absorb iron for survival. This process requires the coordinated action of energy-transducing proteins, transporters, and receptors. The spoilage factors of some spoilage bacteria and the pathogenic mechanism of pathogenic bacteria are also closely related to siderophores. Meanwhile, some siderophores have also gradually evolved toward beneficial aspects. First, a variety of siderophores are classified into three aspects. In addition, representative iron uptake systems of Gram-negative and Gram-positive bacteria are described in detail to understand the common and specific pathways of iron uptake by various bacteria. In particular, the causes of siderophore-induced bacterial pathogenicity and the methods and mechanisms of inhibiting bacterial iron absorption under the involvement of siderophores are presented. Then, the application of siderophores in the food sector is mainly discussed, such as improving the food quality of dairy products and meat, inhibiting the attack of pathogenic bacteria on food, improving the plant growth environment, and promoting plant growth. Finally, this review highlights the unresolved fate of siderophores in the iron uptake system and emphasizes further development of siderophore-based substitutes for traditional drugs, new antibiotic-resistance drugs, and vaccines in the food and health sectors.
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Affiliation(s)
- Fangchao Cui
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Rongsen Fan
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Dangfeng Wang
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
- College of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jianrong Li
- College of Food Science and Technology, Bohai University, National & Local Joint Engineering Research Center of Storage, Processing and Safety Control Technology for Fresh Agricultural and Aquatic Products, Jinzhou, China
| | - Tingting Li
- Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, Dalian, China
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11
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Martin JGP, Cotter PD. Filamentous fungi in artisanal cheeses: A problem to be avoided or a market opportunity? Heliyon 2023; 9:e15110. [PMID: 37151695 PMCID: PMC10161367 DOI: 10.1016/j.heliyon.2023.e15110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/24/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The microbial diversity of artisanal cheeses has been ever more extensively explored over recent years. Many new studies have been particularly focused on the detection and identification of fungi associated with cheese rinds. This is not surprising given that the composition and abundance of fungi on the cheese surface can significantly contribute to desirable sensory qualities, while also contributing to defects, particularly during ripening, and risks associated with the production of mycotoxins. Here we critically review the impact of fungi on the quality of artisanal cheeses, as well as the risks associated with the presence of particular species or strains with specific phenotypes. Ultimately, we address the question; should fungi be predominantly considered villains when it comes to artisanal cheese safety or could their presence be better exploited by producers in order to generate innovative products with greater added value? Such discussions will be increasingly important from the perspective of the future commercialization and regulation of artisanal cheeses that frequently contain a high abundance of moulds.
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Affiliation(s)
- José Guilherme Prado Martin
- Microbiology of Fermented Products Laboratory (FERMICRO), Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Corresponding author.
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland and VistaMilk, Ireland
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12
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Perez-Ortiz G, Sidda JD, Peate J, Ciccarelli D, Ding Y, Barry SM. Production of copropophyrin III, biliverdin and bilirubin by the rufomycin producer, Streptomyces atratus. Front Microbiol 2023; 14:1092166. [PMID: 37007481 PMCID: PMC10060970 DOI: 10.3389/fmicb.2023.1092166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/31/2023] [Indexed: 03/18/2023] Open
Abstract
Heme is best known for its role as a versatile prosthetic group in prokaryotic and eukaryotic proteins with diverse biological functions including gas and electron transport, as well as a wide array of redox chemistry. However, free heme and related tetrapyrroles also have important roles in the cell. In several bacterial strains, heme biosynthetic precursors and degradation products have been proposed to function as signaling molecules, ion chelators, antioxidants and photoprotectants. While the uptake and degradation of heme by bacterial pathogens is well studied, less is understood about the physiological role of these processes and their products in non-pathogenic bacteria. Streptomyces are slow growing soil bacteria known for their extraordinary capacity to produce complex secondary metabolites, particularly many clinically used antibiotics. Here we report the unambiguous identification of three tetrapyrrole metabolites from heme metabolism, coproporphyrin III, biliverdin and bilirubin, in culture extracts of the rufomycin antibiotic producing Streptomyces atratus DSM41673. We propose that biliverdin and bilirubin may combat oxidative stress induced by nitric oxide production during rufomycin biosynthesis, and indicate the genes involved in their production. This is, to our knowledge, the first report of the production of all three of these tetrapyrroles by a Streptomycete.
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Affiliation(s)
| | | | | | | | | | - Sarah M. Barry
- Department of Chemistry, Faculty of Natural & Mathematical Sciences, King’s College London, London, United Kingdom
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13
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Involvement of Versatile Bacteria Belonging to the Genus Arthrobacter in Milk and Dairy Products. Foods 2023; 12:foods12061270. [PMID: 36981196 PMCID: PMC10048301 DOI: 10.3390/foods12061270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/13/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Milk is naturally a rich source of many essential nutrients; therefore, it is quite a suitable medium for bacterial growth and serves as a reservoir for bacterial contamination. The genus Arthrobacter is a food-related bacterial group commonly present as a contaminant in milk and dairy products as primary and secondary microflora. Arthrobacter bacteria frequently demonstrate the nutritional versatility to degrade different compounds even in extreme environments. As a result of their metabolic diversity, Arthrobacter species have long been of interest to scientists for application in various industry and biotechnology sectors. In the dairy industry, strains from the Arthrobacter genus are part of the microflora of raw milk known as an indicator of hygiene quality. Although they cause spoilage, they are also regarded as important strains responsible for producing fermented milk products, especially cheeses. Several Arthrobacter spp. have reported their significance in the development of cheese color and flavor. Furthermore, based on the data obtained from previous studies about its thermostability, and thermoacidophilic and thermoresistant properties, the genus Arthrobacter promisingly provides advantages for use as a potential producer of β-galactosidases to fulfill commercial requirements as its enzymes allow dairy products to be treated under mild conditions. In light of these beneficial aspects derived from Arthrobacter spp. including pigmentation, flavor formation, and enzyme production, this bacterial genus is potentially important for the dairy industry.
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14
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Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532449. [PMID: 36993360 PMCID: PMC10054941 DOI: 10.1101/2023.03.13.532449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecule mediated BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis spp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and their role in complex communities should continue to be a priority.
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Affiliation(s)
- Gordon T. Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Jessica C. Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612
| | - Emily C. Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Celine A. Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
- Tufts University Sensory and Science Center, Medford Massachusetts, 02155
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607
| | - Rachel J. Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
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15
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Graffius S, Garzón JFG, Zehl M, Pjevac P, Kirkegaard R, Flieder M, Loy A, Rattei T, Ostrovsky A, Zotchev SB. Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris. Microbiol Spectr 2023; 11:e0435322. [PMID: 36728429 PMCID: PMC10100984 DOI: 10.1128/spectrum.04353-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023] Open
Abstract
Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.
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Affiliation(s)
- Sophie Graffius
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
| | | | - Martin Zehl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Rasmus Kirkegaard
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Mathias Flieder
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Alexander Loy
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, University of Vienna, Vienna, Austria
- Department of Microbiology and Ecosystem Science, Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Thomas Rattei
- Department of Microbiology and Ecosystem Science, Division of Computational System Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Andrew Ostrovsky
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, Geozentrum, University of Vienna, Vienna, Austria
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Sergey B. Zotchev
- Department of Pharmaceutical Sciences, Division of Pharmacognosy, University of Vienna, Vienna, Austria
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16
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Karthik Y, Ishwara Kalyani M, Krishnappa S, Devappa R, Anjali Goud C, Ramakrishna K, Wani MA, Alkafafy M, Hussen Abduljabbar M, Alswat AS, Sayed SM, Mushtaq M. Antiproliferative activity of antimicrobial peptides and bioactive compounds from the mangrove Glutamicibacter mysorens. Front Microbiol 2023; 14:1096826. [PMID: 36876075 PMCID: PMC9982118 DOI: 10.3389/fmicb.2023.1096826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023] Open
Abstract
The Glutamicibacter group of microbes is known for antibiotic and enzyme production. Antibiotics and enzymes produced by them are important in the control, protection, and treatment of chronic human diseases. In this study, the Glutamicibacter mysorens (G. mysorens) strain MW647910.1 was isolated from mangrove soil in the Mangalore region of India. After optimization of growth conditions for G. mysorens on starch casein agar media, the micromorphology of G. mysorens was found to be spirally coiled spore chain, each spore visualized as an elongated cylindrical hairy appearance with curved edges visualized through Field Emission Scanning Electron Microscopy (FESEM) analysis. The culture phenotype with filamentous mycelia, brown pigmentation, and ash-colored spore production was observed. The intracellular extract of G. mysorens characterized through GCMS analysis detected bioactive compounds reported for pharmacological applications. The majority of bioactive compounds identified in intracellular extract when compared to the NIST library revealed molecular weight ranging below 1kgmole-1. The Sephadex G-10 could result in 10.66 fold purification and eluted peak protein fraction showed significant anticancer activity on the prostate cancer cell line. Liquid Chromatography-Mass Spectrometry (LC-MS) analysis revealed Kinetin-9-ribose and Embinin with a molecular weight below 1 kDa. This study showed small molecular weight bioactive compounds produced from microbial origin possess dual roles, acting as antimicrobial peptides (AMPs) and anticancer peptides (ACPs). Hence, the bioactive compounds produced from microbial origin are a promising source of future therapeutics.
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Affiliation(s)
- Yalpi Karthik
- Department of Studies and Research in Microbiology, Mangalore University, Mangalore, Karnataka, India
| | - Manjula Ishwara Kalyani
- Department of Studies and Research in Microbiology, Mangalore University, Mangalore, Karnataka, India
| | - Srinivasa Krishnappa
- Department of Studies and Research in Biochemistry, Mangalore University, Mangalore, Karnataka, India
| | - Ramakrishna Devappa
- Dr. C.D Sagar Centre for Life Sciences, Biotechnology Department, Dayananda Sagar College of Engineering, Dayananda Sagar Institutions, Bengaluru, India
| | - Chengeshpur Anjali Goud
- Department of Plant Biotechnology, School of Agricultural Sciences, Malla Reddy University, Hyderabad, India
| | - Krishnaveni Ramakrishna
- Department of Studies and Research in Microbiology, Vijayanagara Sri Krishnadevaraya University, Ballari, Karnataka, India
| | - Muneeb Ahmad Wani
- Division of Floriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Srinagar, Jammu and Kashmir, India
| | - Mohamed Alkafafy
- Department of Cytology and Histology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Maram Hussen Abduljabbar
- Department of Pharmacology and Toxicology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Amal S Alswat
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Samy M Sayed
- Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Muntazir Mushtaq
- ICAR-National Bureau of Plant Genetic Resources, Division of Germplasm Evaluation, New Delhi, India.,MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management, Bajhol, Himachal Pradesh, India
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17
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Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition. Int J Mol Sci 2022; 23:ijms232315248. [PMID: 36499572 PMCID: PMC9740669 DOI: 10.3390/ijms232315248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor, grown from its refuge area in the Fertile Crescent, were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR), upon interaction with an elite wheat cultivar. In nitrogen-starved plants, they increased the amount of nitrogen in the seed crop (per plant) by about twofold. A bacterial growth medium was developed to investigate the effects of bacterial exudates on root development in the elite cultivar, and to analyze the exo-metabolomes and exo-proteomes. Altered root development was observed, with distinct responses depending on the strain, for instance, with respect to root hair development. A first conclusion from these results is that the ability of wheat to establish effective beneficial interactions with PGPRs does not appear to have undergone systematic deep reprogramming during domestication. Exo-metabolome analysis revealed a complex set of secondary metabolites, including nutrient ion chelators, cyclopeptides that could act as phytohormone mimetics, and quorum sensing molecules having inter-kingdom signaling properties. The exo-proteome-comprised strain-specific enzymes, and structural proteins belonging to outer-membrane vesicles, are likely to sequester metabolites in their lumen. Thus, the methodological processes we have developed to collect and analyze bacterial exudates have revealed that PGPRs constitutively exude a highly complex set of metabolites; this is likely to allow numerous mechanisms to simultaneously contribute to plant growth promotion, and thereby to also broaden the spectra of plant genotypes (species and accessions/cultivars) with which beneficial interactions can occur.
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18
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Schneider YK, Hagestad OC, Li C, Hansen EH, Andersen JH. Selective isolation of Arctic marine actinobacteria and a down-scaled fermentation and extraction strategy for identifying bioactive compounds. Front Microbiol 2022; 13:1005625. [DOI: 10.3389/fmicb.2022.1005625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
Actinobacteria are among the most prolific producers of bioactive secondary metabolites. In order to collect Arctic marine bacteria for the discovery of new bioactive metabolites, actinobacteria were selectively isolated during a research cruise in the Greenland Sea, Norwegian Sea and the Barents Sea. In the frame of the isolation campaign, it was investigated how different sample treatments, isolation media and sample-sources, such as animals and sediments, affected the yield of actinobacterial isolates to aid further isolation campaigns. Special attention was given to sediments, where we expected spores of spore forming bacteria to enrich. Beside actinobacteria a high share of bacilli was obtained which was not desired. An experimental protocol for down-scaled cultivation and extraction was tested and compared with an established low-throughput cultivation and extraction protocol. The heat-shock method proved suitable to enrich spore-, or endospore forming bacteria such as bacilli. Finally, a group bioactive compounds could be tentatively identified using UHPLC–MS/MS analysis of the active fractions.
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19
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Cryptic specialized metabolites drive Streptomyces exploration and provide a competitive advantage during growth with other microbes. Proc Natl Acad Sci U S A 2022; 119:e2211052119. [PMID: 36161918 DOI: 10.1073/pnas.2211052119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces bacteria have a complex life cycle that is intricately linked with their remarkable metabolic capabilities. Exploration is a recently discovered developmental innovation of these bacteria, that involves the rapid expansion of a structured colony on solid surfaces. Nutrient availability impacts exploration dynamics, and we have found that glycerol can dramatically increase exploration rates and alter the metabolic output of exploring colonies. We show here that glycerol-mediated growth acceleration is accompanied by distinct transcriptional signatures and by the activation of otherwise cryptic metabolites including the orange-pigmented coproporphyrin, the antibiotic chloramphenicol, and the uncommon, alternative siderophore foroxymithine. Exploring cultures are also known to produce the well-characterized desferrioxamine siderophore. Mutational studies of single and double siderophore mutants revealed functional redundancy when strains were cultured on their own; however, loss of the alternative foroxymithine siderophore imposed a more profound fitness penalty than loss of desferrioxamine during coculture with the yeast Saccharomyces cerevisiae. Notably, the two siderophores displayed distinct localization patterns, with desferrioxamine being confined within the colony area, and foroxymithine diffusing well beyond the colony boundary. The relative fitness advantage conferred by the alternative foroxymithine siderophore was abolished when the siderophore piracy capabilities of S. cerevisiae were eliminated (S. cerevisiae encodes a ferrioxamine-specific transporter). Our work suggests that exploring Streptomyces colonies can engage in nutrient-targeted metabolic arms races, deploying alternative siderophores that allow them to successfully outcompete other microbes for the limited bioavailable iron during coculture.
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20
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Draft Genome Sequence of
Glutamicibacter
sp. Strain JC586, Isolated from Soil Sediment of the Floating Islands of Loktak Lake, India. Microbiol Resour Announc 2022; 11:e0074622. [PMID: 36125284 PMCID: PMC9583790 DOI: 10.1128/mra.00746-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The 3.52-Mbp whole-genome sequence of a Glutamicibacter sp. strain isolated from soil sediment of the floating islands of Loktak Lake is reported. The genomic information here gives insight into the presence of genes linked to oxidative stress, osmo-protection, and cold shock proteins which helps in the survival of the organism under extreme environmental conditions.
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21
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A review of methods for the inference and experimental confirmation of microbial association networks in cheese. Int J Food Microbiol 2022; 368:109618. [DOI: 10.1016/j.ijfoodmicro.2022.109618] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/21/2022] [Accepted: 03/06/2022] [Indexed: 12/15/2022]
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22
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Pierce EC, Dutton RJ. Putting microbial interactions back into community contexts. Curr Opin Microbiol 2022; 65:56-63. [PMID: 34739927 DOI: 10.1016/j.mib.2021.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/31/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
Microbial interactions are key aspects of the biology of microbiomes. Recently, there has been a shift in the field towards studying interactions in more representative contexts, whether using multispecies model microbial communities or by looking at interactions in situ. Across diverse microbial systems, these studies have begun to identify common interaction mechanisms. These mechanisms include interactions related to toxic molecules, nutrient competition and cross-feeding, access to metals, signaling pathways, pH changes, and interactions within biofilms. Leveraging technological innovations, many of these studies have used an interdisciplinary approach combining genetic, metabolomic, imaging, and/or microfluidic techniques to gain insight into mechanisms of microbial interactions and into the impact of these interactions on microbiomes.
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Affiliation(s)
- Emily C Pierce
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, Jacobs School of Engineering, University of California, San Diego, La Jolla, USA.
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23
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Identification of Red Pigments Produced by Cheese-Ripening Bacterial Strains of Glutamicibacter arilaitensis Using HPLC. DAIRY 2021. [DOI: 10.3390/dairy2030031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Glutamicibacter arilaitensis is one of the predominant bacterial species involved in the coloration of cheese rinds, especially smear-ripened cheeses. Besides well-known yellow-pigmented carotenoids, this species exhibits an ability to produce red pigments, as the occurrence of pink/red formation was previously found when co-cultured with a fungal strain. In this work, the red pigments synthesized by G. arilaitensis strains grown on cheese-based (curd) solid medium deacidified using Debaryomyces hansenii were identified. The analyses using HPLC equipped with both fluorescence and diode array detectors were performed to characterize the pigments extracted from a dry matter of the medium inoculated with either G. arilaitensis Re117, Po102, or Stp101. Based on the UV–vis absorption spectra, the elution order, and fluorescent property, compared to those of the porphyrin standards, eight metal-free porphyrins, including UPI, UPIII, 7PI, 6PI, 5PI, CPI, CPIII, and MPIX, were indicated as components of the red pigments produced by these G. arilaitensis strains. However, following the chromatographic profiles, the degree of porphyrins formed by each strain was apparently different. Regardless of precise quantitative measurement, the type strains Re117 and Po102 manifested a potential to produce a high amount of CPIII, whereas MPIX was formed by the strains Po102 and Stp101, but exceptionally high by the strain Stp101. The variation in both yield and form of the red pigments synthesized by the cheese-related bacterial G. arilaitensis has not previously been reported; therefore, our results provide the first information on these aspects.
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24
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Cosetta CM, Wolfe BE. Deconstructing and Reconstructing Cheese Rind Microbiomes for Experiments in Microbial Ecology and Evolution. ACTA ACUST UNITED AC 2021; 56:e95. [PMID: 31891451 DOI: 10.1002/cpmc.95] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cheese rind microbiomes are useful model systems for identifying the mechanisms that control microbiome diversity. Here, we describe the methods we have optimized to first deconstruct in situ cheese rind microbiome diversity and then reconstruct that diversity in laboratory environments to conduct controlled microbiome manipulations. Most cheese rind microbial species, including bacteria, yeasts, and filamentous fungi, can be easily cultured using standard lab media. Colony morphologies of taxa are diverse and can often be used to distinguish taxa at the phylum and sometimes even genus level. Through the use of cheese curd agar medium, thousands of unique community combinations or microbial interactions can be assessed. Transcriptomic experiments and transposon mutagenesis screens can pinpoint mechanisms of interactions between microbial species. Our general approach of creating a tractable synthetic microbial community from cheese can be easily applied to other fermented foods to develop other model microbiomes. © 2019 by John Wiley & Sons, Inc. Basic Protocol 1: Isolation of cheese rind microbial communities Support Protocol 1: Preparation of plate count agar with milk and salt Basic Protocol 2: Identification of cheese rind bacterial and fungal isolates using 16S and ITS sequences Basic Protocol 3: Preparation of experimental glycerol stocks of yeasts and bacteria Basic Protocol 4: Preparation of experimental glycerol stocks of filamentous fungi Basic Protocol 5: Reconstruction of cheese rind microbial communities in vitro Support Protocol 2: Preparation of lyophilized and powdered cheese curd Support Protocol 3: Preparation of 10% cheese curd agar plates and tubes Basic Protocol 6: Interaction screens using responding lawns Support Protocol 4: Preparation of liquid 2% cheese curd Basic Protocol 7: Experimental evolution Basic Protocol 8: Measuring community function: pH/acidification Basic Protocol 9: Measuring community function: Pigment production Basic Protocol 10: RNA sequencing of cheese rind biofilms.
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Affiliation(s)
- Casey M Cosetta
- Department of Biology, Tufts University, Medford, Massachusetts
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Mayo B, Rodríguez J, Vázquez L, Flórez AB. Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety. Foods 2021; 10:602. [PMID: 33809159 PMCID: PMC8000492 DOI: 10.3390/foods10030602] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/09/2021] [Indexed: 12/26/2022] Open
Abstract
The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.
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Affiliation(s)
- Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300 Villaviciosa, Spain; (J.R.); (L.V.); (A.B.F.)
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Abstract
The complexity of animal microbiomes presents challenges to defining signaling molecules within the microbial consortium and between the microbes and the host. By focusing on the binary symbiosis between Vibrio fischeri and Euprymna scolopes, we have combined genetic analysis with direct imaging to define and study small molecules in the intact symbiosis. The lifelong relationship between the Hawaiian bobtail squid Euprymna scolopes and its microbial symbiont Vibrio fischeri represents a simplified model system for studying microbiome establishment and maintenance. The bacteria colonize a dedicated symbiotic light organ in the squid, from which bacterial luminescence camouflages the host in a process termed counterillumination. The squid host hatches without its symbionts, which must be acquired from the ocean amidst a diversity of nonbeneficial bacteria, such that precise molecular communication is required for initiation of the specific relationship. Therefore it is likely there are specialized metabolites used in the light organ microenvironment to modulate these processes. To identify small molecules that may influence the establishment of this symbiosis, we used imaging mass spectrometry to analyze metabolite production in V. fischeri with altered biofilm production, which correlates directly to colonization capability in its host. “Biofilm-up” and “biofilm-down” mutants were compared to a wild-type strain, and ions that were more abundantly produced by the biofilm-up mutant were detected. Using a combination of structural elucidation and synthetic chemistry, one such signal was determined to be a diketopiperazine, cyclo(d-histidyl-l-proline). This diketopiperazine modulated luminescence in V. fischeri and, using imaging mass spectrometry, was directly detected in the light organ of the colonized host. This work highlights the continued need for untargeted discovery efforts in host-microbe interactions and showcases the benefits of the squid-Vibrio system for identification and characterization of small molecules that modulate microbiome behaviors.
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Martelli F, Bancalari E, Neviani E, Bottari B. Novel insights on pink discoloration in cheese: The case of Pecorino Toscano. Int Dairy J 2020. [DOI: 10.1016/j.idairyj.2020.104829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Jarmusch SA, Lagos-Susaeta D, Diab E, Salazar O, Asenjo JA, Ebel R, Jaspars M. Iron-meditated fungal starvation by lupine rhizosphere-associated and extremotolerant Streptomyces sp. S29 desferrioxamine production. Mol Omics 2020; 17:95-107. [PMID: 33185220 DOI: 10.1039/d0mo00084a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Siderophores are iron-chelating compounds that aid iron uptake, one of the key strategies for microorganisms to carve out ecological niches in microbially diverse environments. Desferrioxamines are the principal siderophores produced by Streptomyces spp. Their biosynthesis has been well studied and as a consequence, the chemical potential of the pathway continues to expand. With all of this in mind, our study aimed to explore extremotolerant and lupine rhizosphere-derived Streptomyces sp. S29 for its potential antifungal capabilities. Cocultivation of isolate S29 was carried out with Aspergillus niger and Botrytis cinerea, both costly fungal phytopathogens in the wine industry, to simulate their interaction within the rhizosphere. The results indicate that not only is Streptomyces sp. S29 extraordinary at producing hydroxamate siderophores but uses siderophore production as a means to 'starve' the fungi of iron. High resolution LC-MS/MS followed by GNPS molecular networking was used to observe the datasets for desferrioxamines and guided structure elucidation of new desferrioxamine analogues. Comparing the new chemistry, using tools like molecular networking and MS2LDA, with the known biosynthesis, we show that the chemical potential of the desferrioxamine pathway has further room for exploration.
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Affiliation(s)
- Scott A Jarmusch
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Old Aberdeen AB24 3UE, Scotland, UK.
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Cosetta CM, Kfoury N, Robbat A, Wolfe BE. Fungal volatiles mediate cheese rind microbiome assembly. Environ Microbiol 2020; 22:4745-4760. [PMID: 32869420 DOI: 10.1111/1462-2920.15223] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/28/2020] [Accepted: 08/28/2020] [Indexed: 12/01/2022]
Abstract
In vitro studies in plant, soil, and human systems have shown that microbial volatiles can mediate microbe-microbe or microbe-host interactions. These previous studies have often used artificially high concentrations of volatiles compared to in situ systems and have not demonstrated the roles volatiles play in mediating community-level dynamics. We used the notoriously volatile cheese rind microbiome to identify bacteria responsive to volatiles produced by five widespread cheese fungi. Vibrio casei had the strongest growth stimulation when exposed to all fungi. In multispecies community experiments, fungal volatiles caused a shift to a Vibrio-dominated community, potentially explaining the widespread occurrence of Vibrio in surface-ripened cheeses. RNA sequencing identified activation of the glyoxylate shunt as a possible mechanism underlying volatile-mediated growth promotion and community assembly. Our study demonstrates how airborne chemicals could be used to control the composition of microbiomes and illustrates how volatiles may impact the development of cheese rinds.
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Affiliation(s)
- Casey M Cosetta
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA
| | - Nicole Kfoury
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Albert Robbat
- Department of Chemistry, Tufts University, 62 Talbot Ave., Medford, MA, 02155, USA
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, 200 Boston Ave, Medford, MA, 02155, USA
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Wakimoto T, Nakagishi S, Matsukawa N, Tani S, Kai K. A Unique Combination of Two Different Quorum Sensing Systems in the β-Rhizobium Cupriavidus taiwanensis. JOURNAL OF NATURAL PRODUCTS 2020; 83:1876-1884. [PMID: 32484353 DOI: 10.1021/acs.jnatprod.0c00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cupriavidus taiwanensis LMG19424, a β-rhizobial symbiont of Mimosa pudica, harbors phc and tqs quorum sensing (QS), which are the homologous cell-cell communication systems previously identified from the plant pathogen Ralstonia solanacearum and the human pathogen Vibrio cholerae, respectively. However, there has been no experimental evidence reported that these QS systems function in C. taiwanensis LMG19424. We identified (R)-methyl 3-hydroxymyristate (3-OH MAME) and (S)-3-hydroxypentadecan-4-one (C15-AHK) as phc and tqs QS signals, respectively, and characterized these QS systems. The expression of the signal synthase gene phcB and tqsA in E. coli BL21(DE3) resulted in the high production of 3-OH MAME and C15-AHK, respectively. Their structures were elucidated by comparison of EI-MS data and GC/chiral LC retention times with synthetic standards. The deletion of phcB reduced cell motility and increased biofilm formation, and the double deletion of phcB/tqsA caused the accumulation of the metal chelator coproporphyrin III in its mutant culture. Although the deletion of phcB and tqsA slightly reduced its ability to nodulate on aseptically grown seedlings of M. pudica, there was no significant difference in nodule formation between LMG19424 and its QS mutants when commercial soils were used. Taken together, this is the first example of the simultaneous production of 3-OH MAME/C15-AHK as QS signals in a bacterial species, and the importance of the phc/tqs QS systems in the saprophytic stage of C. taiwanensis LMG19424 is suggested.
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Affiliation(s)
- Takayuki Wakimoto
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Shiori Nakagishi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Nao Matsukawa
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Shuji Tani
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Kenji Kai
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
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Spraker JE, Luu GT, Sanchez LM. Imaging mass spectrometry for natural products discovery: a review of ionization methods. Nat Prod Rep 2020; 37:150-162. [PMID: 31364647 PMCID: PMC6992513 DOI: 10.1039/c9np00038k] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Covering: 2009-2019 Over the last decade, methods in imaging mass spectrometry (IMS) have progressively improved and diversified toward a variety of applications in natural products research. Because IMS allows for the spatial mapping of the production and distribution of biologically active molecules in situ, it facilitates phenotype and organelle driven discovery efforts. As practitioners of IMS for natural products discovery, we find one of the most important aspects of these experiments is the sample preparation and compatibility with different ionization sources that are available to a given researcher. As such, we have focused this mini review to cover types of ionization sources that have been used in natural products discovery applications and provided concrete examples of use for natural products discovery while discussing the advantages and limitations of each method. We aim for this article to serve as a resource to guide the broader natural product community interested in IMS toward the application/method that would best serve their natural product discovery needs given the sample and analyte(s) of interest. This mini review has been limited to applications using natural products and thus is not exhaustive of all possible ionization methods which have only been applied to image other types of samples such as mammalian tissues. Additionally, we briefly review how IMS has been coupled with other imaging platforms, such as microscopy, to enhance information outputs as well as offer our future perspectives on the incorporation of IMS in natural products discovery.
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Affiliation(s)
- Joseph E Spraker
- Hexagon Bio, 1505 Adams Drive, Suite A, Menlo Park, CA 94025, USA
| | - Gordon T Luu
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA,
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA,
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Exploration of cryptic organic photosensitive compound as Zincphyrin IV in Streptomyces venezuelae ATCC 15439. Appl Microbiol Biotechnol 2019; 104:713-724. [PMID: 31820068 DOI: 10.1007/s00253-019-10262-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/07/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022]
Abstract
Zincphyrin IV is a potential organic photosensitizer which is of significant interest for applications in biomedicine, materials science, agriculture (as insecticide), and chemistry. Most studies on Zincphyrin are focused on Zincphyrin III while biosynthesis and application of Zincphyrin IV is comparatively less explored. In this study, we explored Zincphyrin IV production in Streptomyces venezuelae ATCC 15439 through combination of morphology engineering and "One strain many compounds" approach. The morphology engineering followed by change in culture medium led to activation of cryptic Zincphyrin IV biosynthetic pathway in S. venezuelae with subsequent detection of Zincphyrin IV. Morphology engineering applied in S. venezuelae increased the biomass from 7.17 to 10.5 mg/mL after 48 h of culture. Moreover, morphology of engineered strain examined by SEM showed reduced branching and fragmentation of mycelia. The distinct change in color of culture broth visually demonstrated the activation of the cryptic biosynthetic pathway in S. venezuelae. The production of Zincphyrin IV was found to be initiated after overexpression ssgA, resulting in the increase in titer from 4.21 to 7.54 μg/mL. Furthermore, Zincphyrin IV demonstrated photodynamic antibacterial activity against Bacillus subtilis and photodynamic anticancer activity against human ovarian carcinoma cell lines.
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Glutamicibacter mishrai sp. nov., isolated from the coral Favia veroni from Andaman Sea. Arch Microbiol 2019; 202:733-745. [PMID: 31796989 DOI: 10.1007/s00203-019-01783-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 11/25/2019] [Indexed: 10/25/2022]
Abstract
A novel aerobic marine actinobacterium (strain S5-52T) belonging to the genus Glutamicibacter was isolated from the coral Favia veroni sampled from the Andaman Sea, India. Cells are Gram stain positive and rod shaped. The DNA G+C content was 58.7 mol%. The major quinones were MK-8 and MK-9. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid, trimannosyldiacylglycerol, phospholipid and dimannosylglyceride. The peptidoglycan type was A4α. Strain S5-52T showed a maximum 16S rRNA similarity of 99.36% with Glutamicibacter halophytocola DSM 101718T. The genome of strain S5-52T was 3.57 Mb that contains 3274 protein coding sequences (CDS). DNA-DNA similarity and ANI values between S5-52T and the reference strains were below 70% and 95-96%, respectively. Analysis of genomic reduction events in the evolutionary path from the LUCA (last universal common ancestor) to G. mishrai LMG 29155T and G. halophytocola DSM 101718T exhibit a number of genes involved in amino acid metabolism, cell wall biogenesis and replication, recombination and repair mechanism that reduced in both the species. Based on phenotypic, chemotaxonomic properties and comparative genomic studies, the strain S5-52T is considered a novel species of the genus Glutamicibacter, for which the name Glutamicibacter mishrai sp. nov. is proposed. The type strain is S5-52T (= KCTC 39846T = LMG 29155T).
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Cosetta CM, Wolfe BE. Causes and consequences of biotic interactions within microbiomes. Curr Opin Microbiol 2019; 50:35-41. [PMID: 31627129 DOI: 10.1016/j.mib.2019.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 08/20/2019] [Accepted: 09/06/2019] [Indexed: 10/25/2022]
Abstract
An integrative pattern-process-mechanism approach is revealing the roles of biotic interactions in microbiome assembly. Patterns of microbiome diversity observed in metagenomic studies can be partly explained by interaction processes (e.g. competition, facilitation) and underlying molecular or genetic mechanisms (e.g. antibiotic production, nutrient cross-feeding). Exciting opportunities remain to fully understand the significance and generalizability of biotic interactions within microbiomes. Many microbial interactions have been studied by chasing easily quantifiable phenotypes including changes in growth or pigmentation, but it is likely that diverse cryptic interactions occur without obvious growth changes or macroscopic phenotypes. A narrow phylogenetic breadth of well-studied microbes limits our understanding of whether there are conserved genetic or molecular mechanisms of microbial interactions. Biotic interactions can impose strong selective pressures that could shape rates and modes of microbial evolution, but few studies have examined the evolutionary consequences of interactions within microbiomes. Continued exploration of the chemical and genetic mechanisms underlying biotic interactions may provide novel tools to manipulate and manage microbiomes.
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Affiliation(s)
- Casey M Cosetta
- Tufts University, Department of Biology, Medford, MA 02155, United States
| | - Benjamin E Wolfe
- Tufts University, Department of Biology, Medford, MA 02155, United States.
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Cleary JL, Luu GT, Pierce EC, Dutton RJ, Sanchez LM. BLANKA: an Algorithm for Blank Subtraction in Mass Spectrometry of Complex Biological Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1426-1434. [PMID: 30993641 PMCID: PMC6675636 DOI: 10.1007/s13361-019-02185-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 05/05/2023]
Abstract
Multispecies microbiome systems are known to be closely linked to human, animal, and plant life processes. The growing field of metabolomics presents the opportunity to detect changes in overall metabolomic profiles of microbial species interactions. These metabolomic changes provide insight into function of metabolites as they correlate to different species presence and the observed phenotypic changes, but detection of subtle changes is often difficult in samples with complex backgrounds. Natural environments such as soil and food contain many molecules that convolute mass spectrometry-based analyses, and identification of microbial metabolites amongst environmental metabolites is an informatics problem we begin to address here. Our microbes are grown on solid or liquid cheese curd media. This medium, which is necessary for microbial growth, contains high amounts of salts, lipids, and casein breakdown products which make statistical analyses using LC-MS/MS data difficult due to the high background from the media. We have developed a simple algorithm to carry out background subtraction from microbes grown on solid or liquid cheese curd media to aid in our ability to conduct statistical analyses so that we may prioritize metabolites for further structure elucidation. Graphical Abstract .
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Affiliation(s)
- Jessica L Cleary
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St, MC 781, Room 539, Chicago, IL, 60612, USA
| | - Gordon T Luu
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St, MC 781, Room 539, Chicago, IL, 60612, USA
| | - Emily C Pierce
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Dr, La Jolla, CA, 92093, USA
| | - Laura M Sanchez
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S Wood St, MC 781, Room 539, Chicago, IL, 60612, USA.
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The Influence of pH, NaCl, and the Deacidifying Yeasts Debaryomyces hansenii and Kluyveromyces marxianus on the Production of Pigments by the Cheese-Ripening Bacteria Arthrobacter arilaitensis. Foods 2018; 7:foods7110190. [PMID: 30463179 PMCID: PMC6262435 DOI: 10.3390/foods7110190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/18/2022] Open
Abstract
Arthrobacter arilaitensis is a food-related bacterial species under investigation for its involvement in the coloration of surface-ripened cheeses. Presently, information about this species in association with the development of appropriate cheese coloration is still lacking. This study was performed in order to investigate—with the use of spectrocolorimetry—the influence of pH, NaCl, and deacidifying yeasts on the pigmentation of Arthrobacter arilaitensis biofilms. Three types of cheese-based (curd) solid media were prepared by using different deacidification methods: (i) chemical deacidification by NaOH (CMNaOH); (ii) biological deacidification by the yeast strain Debaryomyces hansenii 304 (CMDh304); and (iii) biological deacidification by the yeast strain Kluyveromyces marxianus 44 (CMKm44). Each medium was prepared with initial pH values of 5.8, 7.0, and 7.5. After pasteurization, agar was incorporated and NaCl was added in varying concentrations (0%, 2%, 4%, and 8% (w/v)). A. arilaitensis Po102 was then inoculated on the so prepared “solid-curd” media, and incubated at 12 °C under light conditions for 28 days. According to the data obtained by spectrocolorimetry in the Compagnie Internationale de l’Eclairage (CIE) L*a*b* color system, all controlled factors appeared to affect the pigments produced by the A. arilaitensis strain. NaCl content in the media showed distinct inhibitory effects on the development of color by this strain when the initial pH was at 5.8. By contrast, when the initial pH of the media was higher (7.0, 7.5), only the highest concentration of NaCl (8%) had this effect, while the coloring capacity of this bacterial species was always higher when D. hansenii 304 was used for deacidification compared to K. marxianus 44.
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